5HIX

Cocrystal structure of an anti-parallel DNA G-quadruplex and a tetra-Quinoline Foldamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.

Mandal, P.K.Baptiste, B.Langlois d'Estaintot, B.Kauffmann, B.Huc, I.

(2016) Chembiochem 17: 1911-1914

  • DOI: 10.1002/cbic.201600281

  • PubMed Abstract: 
  • Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antipar ...

    Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antiparallel hairpin dimeric DNA G-quadruplex (G4 T4 G4 )2 with tetramer 1-a helically folded oligo-quinolinecarboxamide bearing cationic side chains-that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G4 T4 G4 )2 in the solid state are observed.


    Organizational Affiliation

    University of Bordeaux, CBMN, UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
Dimeric G-quadruplexA,B12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
61Q
Query on 61Q

Download SDF File 
Download CCD File 
A
4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-nitroquinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinoline-2-carboxylic acid
C52 H52 N12 O11
PDPDTUNURBJNEI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 31.701α = 90.00
b = 31.701β = 90.00
c = 97.373γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFranceERC-2012-AdG-320892

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release